MmuINT0028639 @ mm9
Intron Retention
Gene
ENSMUSG00000024942 | Capn1
Description
calpain 1 [Source:MGI Symbol;Acc:MGI:88263]
Coordinates
chr19:5994560-5994887:-
Coord C1 exon
chr19:5994679-5994887
Coord A exon
chr19:5994600-5994678
Coord C2 exon
chr19:5994560-5994599
Length
79 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CCCTCTTCTCTGCTCTGCAGGGA
3' ss Score
11.04
Exon sequences
Seq C1 exon
CTGGCGGGTCAGCCTGTGCACTTGAAGCGTGATTTCTTCCTGGCCAACGCTTCTCGGGCGCAGTCAGAGCACTTCATCAACCTTCGGGAAGTCAGCAACCGTATCCGCCTGCCGCCCGGGGAGTACATAGTGGTGCCCTCCACCTTCGAGCCCAACAAAGAAGGCGACTTCCTGCTGCGCTTCTTCTCAGAGAAGAAGGCTGGGACCCA
Seq A exon
GTGAGTAGCAGACCCCCATCCTCTCCCACCTCCCTATCTCCCCAGGCCCCTCTGACTGACCCTCTTCTCTGCTCTGCAG
Seq C2 exon
GGAACTAGATGACCAGATCCAGGCCAACCTCCCTGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024942-Capn1:NM_001110504:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.214
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(43.9=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAGTCAGAGCACTTCATCA
R:
TTGGCCTGGATCTGGTCATCT
Band lengths:
178-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: